This section introduces aspects that may help facilitate a better understanding of the disclosure. Accordingly, these statements are to be read in this light and are not to be understood as admissions about what is or is not prior art.
The Coronaviridae family of viruses are enveloped, single-stranded, positive-sense RNA viruses and include 141 species that are classified into four genera according to their phylogenetic relationships: α-, β-, γ-, and δ-coronavirus (FIGS. 1A-1B) (Woo, et al., Exp. Biol. Med. 2009, 234(10):1117-1127). Coronaviruses (CoVs) are zoonotic viruses that infect a variety of animals from whales to birds, bats, cats, and humans. Typically, CoV infection results in mild to moderate respiratory tract infections; however, some CoV species are extremely virulent and can result in widespread fatality. Severe acute respiratory syndrome coronavirus (SARS-CoV) is a human CoV that was responsible for the first pandemic of the 21st century, infecting over 8,000 people with a 10% mortality rate (Perlman, S., et al., Nature Reviews Microbiology 2009, 7(6):439-450). More recently, Middle East respiratory syndrome coronavirus (MERS-CoV) was identified in November 2012 and had since infected over 1,600 people in 26 countries with 36% mortality rate (Chan, et al., J. Formos. Med. Assoc. 2013, 112(7): 372-381).
These especially virulent CoV species arise from interspecies jumping, or zoonotic shifts, which have led to particularly disastrous outbreaks of zoonotic disease. SARS-CoV originated from the Guangdong Province of China in November 2002, where the origin of transmission to humans was identified to be palm civets butchered for food and purchased at exotic animal markets (Xu, et al., Emerg. Infect. Dis. 2004, 10(6):1030-1037; Guan, et al., Science, 2003, 302(5643): 276-278). Horseshoe bats were subsequently identified as the zoonotic reservoir of SARS-CoV (Lau, et al., Proc Natl Acad Sci USA 2005, 102(39):14040-14045). MERS-CoV is also believed to originate from a bat reservoir as it is genetically related to the bat coronaviruses HKU4 and HKU5, and utilizes the same cellular receptor as HKU4 (Yang, et al., Proc Natl Acad Sci USA 2014, 111(34):12516-12521). The origin of MERS-CoV transmission from bats to humans is likely facilitated by dromedary camels as the intermediary host (Reusken, C. B., et al., The Lancet Infectious diseases 2013, 13(10):859-866).
All CoVs express a >800 kDa replicase polyprotein that contains either two or three cysteine proteases, the papain-like protease(s) (PLPpro, or PLP1 and PLP2) and the 3C-like protease (3CLpro, nsp5, or Mpro). These proteases process the CoV replicase polyprotein by cleaving it into 16 non-structural proteins, which are responsible for a variety of aspects of CoV replication (Perlman, S et al., Nature Rev. Microbiol. 2009, 7(6): 439-450). The CoV 3CLpro is responsible for processing 11 cleavage sites of within the replicase polyprotein and is essential for CoV replication, making it a highly valuable target for therapeutic development (Ghosh, et al., J Med Chem 2005, 48(22):6767-6771). Furthermore, the overall active site architecture and substrate recognition pockets are structurally conserved across CoV 3CLpro's, increasing its attractiveness as a target for the development of broad-spectrum anti-CoV therapeutics.
Previous efforts at the design and development of broad-spectrum CoV 3CLpro inhibitors have focused on substrate-mimetic peptidyl inhibitors containing electrophilic warheads capable of covalently reacting with and modifying the 3CLpro catalytic cysteine (Anand, et al., Science 2003, 300(5626): 1763-1767; Kim, et al., J. Virology 2015, 89(9):4942-4950). However, though this class of 3CLpro inhibitors has been known for over a decade, an effective commercially available broad-spectrum therapeutic has yet to be developed. There is a critical need for the development of broad-spectrum CoV therapeutics to overcome the challenges of traditional anti-CoV therapeutic development, as broad-spectrum therapeutics can be rapidly implemented upon zoonotic disease outbreak.